Thank you!
Your support is sustaining the future of local news in our communities.

Antibiotics for gardens and forests: Part I

The title of a recent paper in the Journal of the American Chemical Society, or JACS for short, is: Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Non-ribosomal Lipopeptides Featuring a Transient Amino Acid Building Block. JACS publishes heavy stuff. Readers may think these authors and JACS are on a one-lane road to obscurity, but there is substance here. A shorter title might have been Antibiotics from Pseudomonas Kill Nasty Amoebae and Fungi. The authors named the class of antibiotics after Keanu Reeves, the Canadian actor who plays retired assassin, John Wick, who emerges to kill bad guys. Amoebae and fungi cause many diseases, and they are all bad guys because forestry, agriculture, and medicine have few defenses against them. Fungi kill our crops and trees in periodic waves. I want our ash, chestnut, hemlock, and elm trees back, or at least to give them a fighting chance.

The Jena people, led by Dr. Pierre Stallforth, use a strategy that lets evolution do much of the work. They looked for antibiotics in biological situations where two or more species have fallen into an equilibrium, a condition called either mutualism or competition. They reasoned that one species may make an antibiotic or natural product to compete.

Amoeba-like cells have a lot of internal architecture: vacuoles, nuclei, sites to make special proteins, structures to carry out tasks of digestion and energy production, and ways to recognize harmful bacteria and pull them inside. These cells crawl over the surface of our lungs, peritoneum, and kidneys. They clean up bacteria and debris after inflammation. In the lungs they are called alveolar macrophages, but they patrol almost everywhere. All higher organisms have amoebae or similar cells; they are an essential cellular life form that evolution has kept. Some amoebae can also cause disease; think of amoebic dysentery or the brain destroying amoebae that people get in warm freshwater ponds.

Some amoebae live in a special vacuole, surrounded by a membrane, where they have acquired the ability to interrupt a process that normally kills them. Mycobacterium tuberculosis and Legionella pneumoniae live in such cellular compartments, where they grow and divide. The Stallforth lab uses a species called Dictyostelium discoideum that lives in soil and eats the many bacteria they find there. Legionella and TB bacteria flourish in Dictyostelium the vacuoles of these amoebae.

Your columnist and his lab studied Dictyostelium for decades and wrote a book on these shapeshifting, complicated, and quite beautiful creatures. Type ‘John Bonner and Princeton’ into a browser and you will find a lovely film, made in 1947. Albert Einstein asked to see it. There is more to this story, but let’s return to Dr. Stallworth.

Instead of isolating bacteria or amoebae from this niche and asking if individual bacteria or amoebae produced antibiotics, they extracted DNA and examined the sequences of A, C, G, and T of millions of individual genes. It sounds hard, and it was once, but now the process is efficient and automated. Two classes of genes make the enzymes to produce antibiotics, each easily recognized by their DNA sequences stored in enormous databases. The group found one of them in the bacteria called Pseudomonas.

The story of our niche takes us back to the experimental forest of the University of Virginia in the Great Smoky Mountains, where, in 2014, evolutionary biologists Joan Strassmann and David Quellar of Washington University were looking for new strains of Dictyostelium.

Joan found a fruiting body of Dictyostelium, which looks like a lollipop about 1mm high, but it was on a steaming pile of deer scat. Where the business end of the lollipop would be, there was a ball of tough spores, about 50,000 held in a drop by surface tension. Fruiting bodies form in the lab, but that was the first time one had been seen in the wild. In the liquid around the spores there were bacteria, a strain of Pseudomonas, now called QS1027 (Queller-Strassmann), that we now know secretes antibiotics.

Let me leave you with Professor Joan Strassmann, author of a recent book called Slow Birding, a member of The National Academic of Sciences, a teacher and mentor, on hands and knees with her nose six inches from a heap of deer poop, yelling in delight. Joy is where you find it.

Richard Kessin, Ph.D, is Emeritus Professor of Pathology and Cell Biology in the Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical center. His columns are at RichardKessin.com.

The views expressed here are not necessarily those of The Lakeville Journal and The Journal does not support or oppose candidates for public office.

Latest News

Yerger Johnstone

Yerger Johnstone

SHARON — Yerger Johnstone, former managing director in the mergers and acquisitions department at Morgan Stanley and a decorated veteran of the Vietnam War, died on April 19, 2026, in Chelmsford, England. He was 86.

Born in Mobile, Alabama, on March 7, 1940, Mr. Johnstone was the son of architect Henry Inge Johnstone, architect, and Kathleen Yerger Johnstone, the noted nature writer and civic leader after whom Alabama’s state seashell, Johnstone’s Junonia, is named. He graduated from Murphy High School in Mobile in 1958, received his bachelor’s degree from the University of the South at Sewanee in 1962, and earned his M.B.A. from the University of Chicago Booth School of Business in 1964.

Keep ReadingShow less

Richard R. Stover

Richard R. Stover

WEST CORNWALL — Richard R. Stover, 82, of West Cornwall, died peacefully at Noble Horizons on May 26, 2026.

Son of the late Robert and Leona (Heinbockel) Stover, Rick was born Feb. 6, 1944 in Edina, Minnesota. He attended the University of Pennsylvania where he majored in Economics and was a member of Sigma Alpha Epsilon fraternity.

Keep ReadingShow less

Floyd Irving Isham

Floyd Irving Isham

SHARON — Floyd Irving Isham Jr., 87, a longtime area resident, died Tuesday, May 26, 2026, at Sharon Health Care Center in Sharon. Mr. Isham worked for the Tri-Wall Container Corp. in Wassaic, New York, for fifteen years and also worked as a self-employed private caretaker for over twenty-five years, caring for local estates in Shekomeko, Pine Plains and Ancramdale, New York, prior to his retirement.

Born Aug. 25, 1938, in St. George, Vermont, he was the son of the late Floyd Irving and Hazel (Thompson) Isham, Sr. Following his high school years, he enlisted in the United States Navy and served from 1958 until his honorable discharge in 1961. Mr. Isham also served in the Vermont National Guard. On Aug. 11, 1990, in Dover Plains, New York, he married Nancy L. Cross. Mrs. Isham died on July 8, 2005.

Keep ReadingShow less
google preferred source

Want more of our stories on Google? Click here to make us a Preferred Source.

Pauline King Garfield

Pauline King Garfield

EAST CANAAN — Pauline K. (King) Garfield, 94 of 77 South Canaan Rd. formerly of East Canaan, died Sunday May 24, 2026, at Geer Village. She was the wife of the late Duane Garfield who passed August 14, 2017. Pauline was born April 3, 1932 in North Canaan,in the former Geer Hospital. She was the daughter of the late Charles and Rose (Van Vlack) King.

Pauline spent her career at Becton Dickinson in Canaan, after being a stay-at-home mother for many years.She was employed at Becton Dickinson for 23 years. She enjoyed bus trips with her late husband Duane to the Casinos, spending time with her family watching the grandchildren grow up. Recently she made a comment to care givers that was “wait until I see that husband of mine for leaving me here, I am going to read him the riot act.” Over the years she enjoyed many crafts, but her favorite was crocheting gifts for everyone.

Keep ReadingShow less
Great Country Mutt Show returns as animal shelter surrenders rise

Great Dane “Axel” with owner Sage Breyette in the Best Lap Dog Over 40 lbs. contest at last year’s Great Country Mutt Show

Aly Morrissey

Tail wags, floppy ears and a healthy dose of canine charm will take center stage June 7 as The Little Guild hosts its annual Great Country Mutt Show at Lime Rock Park in Falls Village.

Last year’s Great Country Mutt Show attracted more than 200 dogs and 800 people. Founded by renowned designer Bunny Williams as a benefit for the Little Guild, the tongue-in-cheek, Westminster-style event has grown into one of the organization’s signature annual fundraisers and community celebrations. The show remains free and open to the public, and adoptable dogs may attend when appropriate.

Keep ReadingShow less

Savannah Stevenson’s second act

Savannah Stevenson’s second act

Savannah Stevenson as Mrs. Paroo and Elliott Andrews who plays Harold Hill in the nationally touring production of “The Music Man.”

Marshall Meadows
Sharing laughter, tears, music and dancing through stories that illuminate our common humanity touches us in a way that builds connection, empathy and genuine community.
— Savannah Stevenson

Savannah Stevenson has lived enough lives already to make most people feel lazy.

She grew up in Atlanta in a musical family, with a father who played “The Sound of Music” cassette tapes in the car and a mother who played hymns on the piano. She went to Carnegie Mellon to study musical theater, moved to New York afterward and, for a while, imagined a life onstage.

Keep ReadingShow less
google preferred source

Want more of our stories on Google? Click here to make us a Preferred Source.

google preferred source

Want more of our stories on Google? Click here to make us a Preferred Source.